Design and immunogenic evaluation of multi-epitope vaccines for colorectal cancer: insights from molecular dynamics and In-Vitro studies
BackgroundThis study aimed to identify cytotoxic T lymphocyte (CTL)-specific epitopes from three tumor-associated antigens (TAAs)—Dickkopf-like 1 (DKKL1), F-box protein 39 (FBXO39), and Opa-interacting protein 5 (OIP5)—which are overexpressed in colorectal cancer (CRC), as potential candidates for C...
Saved in:
| Main Authors: | , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Frontiers Media S.A.
2025-06-01
|
| Series: | Frontiers in Oncology |
| Subjects: | |
| Online Access: | https://www.frontiersin.org/articles/10.3389/fonc.2025.1592072/full |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1850220064693813248 |
|---|---|
| author | Peiwei Sun Luolin Wang Zhong Liu Zhenglei Xu |
| author_facet | Peiwei Sun Luolin Wang Zhong Liu Zhenglei Xu |
| author_sort | Peiwei Sun |
| collection | DOAJ |
| description | BackgroundThis study aimed to identify cytotoxic T lymphocyte (CTL)-specific epitopes from three tumor-associated antigens (TAAs)—Dickkopf-like 1 (DKKL1), F-box protein 39 (FBXO39), and Opa-interacting protein 5 (OIP5)—which are overexpressed in colorectal cancer (CRC), as potential candidates for CTL-mediated immunotherapy.MethodsThe amino acid sequences of DKKL1, FBXO39, and OIP5 were analyzed to predict high-affinity CTL epitopes using the NetCTL server. Their antigenicity, allergenicity, conservation, and glycosylation potential were assessed for safety and effectiveness. Cross-reactivity and binding affinities were evaluated through molecular docking. Two multi-epitope vaccine constructs were designed incorporating the CTL epitopes, GM-CSF and IL-2 adjuvants, and a PADRE sequence. Docking studies with Toll-like receptor 4 (TLR-4) were performed. In-vitro assays using human peripheral blood mononuclear cells (PBMCs) were conducted to evaluate the immunogenicity of the vaccine constructs, focusing on cytokine release and T-cell activation. Additionally, molecular dynamics simulations were performed to assess the stability of peptide-HLA interactions.ResultsHigh-affinity CTL-specific epitopes were successfully identified from DKKL1, FBXO39, and OIP5, showing strong binding potential to HLA class I molecules. The selected epitopes were predicted to be non-allergenic, non-glycosylated, and conserved across species. Molecular docking confirmed stable binding interactions between the epitopes and HLA alleles. In-vitro validation demonstrated that PBMCs stimulated with the multi-epitope vaccine constructs produced significant increase in cytokine levels, including IFN-γ and IL-2, indicative of robust CTL activation. Moreover, molecular dynamics simulations showed strong and stable binding affinities between the epitopes and HLA molecules, suggesting effective antigen presentation. Additionally, docking studies revealed strong binding affinities between the vaccine constructs and TLR-4, suggesting their potential to trigger a strong immune response.ConclusionThis study identified CTL-specific epitopes from DKKL1, FBXO39, and OIP5 as potential targets for colorectal cancer immunotherapy. The multi-epitope vaccine constructs exhibited significant immunogenic potential, providing a foundation for future clinical validation. These findings underscore the promise of these TAAs as key targets for CTL-based vaccine development in colorectal cancer. |
| format | Article |
| id | doaj-art-a4c74a8f36f148cd9d5cf8b8027cca54 |
| institution | OA Journals |
| issn | 2234-943X |
| language | English |
| publishDate | 2025-06-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Oncology |
| spelling | doaj-art-a4c74a8f36f148cd9d5cf8b8027cca542025-08-20T02:07:12ZengFrontiers Media S.A.Frontiers in Oncology2234-943X2025-06-011510.3389/fonc.2025.15920721592072Design and immunogenic evaluation of multi-epitope vaccines for colorectal cancer: insights from molecular dynamics and In-Vitro studiesPeiwei Sun0Luolin Wang1Zhong Liu2Zhenglei Xu3Department of General Surgery, Shenzhen University General Hospital/Shenzhen University Clinical Medical Academy, Shenzhen, ChinaDepartment of Gastroenterology, Shenzhen People's Hospital (The First Affiliated Hospital, Southern University of Science and Technology; The Second Clinical Medical College, Jinan University), Shenzhen, Guangdong, ChinaDepartment of General Surgery, Shenzhen University General Hospital/Shenzhen University Clinical Medical Academy, Shenzhen, ChinaDepartment of Gastroenterology, Shenzhen People's Hospital (The First Affiliated Hospital, Southern University of Science and Technology; The Second Clinical Medical College, Jinan University), Shenzhen, Guangdong, ChinaBackgroundThis study aimed to identify cytotoxic T lymphocyte (CTL)-specific epitopes from three tumor-associated antigens (TAAs)—Dickkopf-like 1 (DKKL1), F-box protein 39 (FBXO39), and Opa-interacting protein 5 (OIP5)—which are overexpressed in colorectal cancer (CRC), as potential candidates for CTL-mediated immunotherapy.MethodsThe amino acid sequences of DKKL1, FBXO39, and OIP5 were analyzed to predict high-affinity CTL epitopes using the NetCTL server. Their antigenicity, allergenicity, conservation, and glycosylation potential were assessed for safety and effectiveness. Cross-reactivity and binding affinities were evaluated through molecular docking. Two multi-epitope vaccine constructs were designed incorporating the CTL epitopes, GM-CSF and IL-2 adjuvants, and a PADRE sequence. Docking studies with Toll-like receptor 4 (TLR-4) were performed. In-vitro assays using human peripheral blood mononuclear cells (PBMCs) were conducted to evaluate the immunogenicity of the vaccine constructs, focusing on cytokine release and T-cell activation. Additionally, molecular dynamics simulations were performed to assess the stability of peptide-HLA interactions.ResultsHigh-affinity CTL-specific epitopes were successfully identified from DKKL1, FBXO39, and OIP5, showing strong binding potential to HLA class I molecules. The selected epitopes were predicted to be non-allergenic, non-glycosylated, and conserved across species. Molecular docking confirmed stable binding interactions between the epitopes and HLA alleles. In-vitro validation demonstrated that PBMCs stimulated with the multi-epitope vaccine constructs produced significant increase in cytokine levels, including IFN-γ and IL-2, indicative of robust CTL activation. Moreover, molecular dynamics simulations showed strong and stable binding affinities between the epitopes and HLA molecules, suggesting effective antigen presentation. Additionally, docking studies revealed strong binding affinities between the vaccine constructs and TLR-4, suggesting their potential to trigger a strong immune response.ConclusionThis study identified CTL-specific epitopes from DKKL1, FBXO39, and OIP5 as potential targets for colorectal cancer immunotherapy. The multi-epitope vaccine constructs exhibited significant immunogenic potential, providing a foundation for future clinical validation. These findings underscore the promise of these TAAs as key targets for CTL-based vaccine development in colorectal cancer.https://www.frontiersin.org/articles/10.3389/fonc.2025.1592072/fullcolorectal cancercytotoxic T lymphocyteDickkopf-like 1 proteinF-box protein 39Opa-interacting protein 5Toll-Like Receptor 4 |
| spellingShingle | Peiwei Sun Luolin Wang Zhong Liu Zhenglei Xu Design and immunogenic evaluation of multi-epitope vaccines for colorectal cancer: insights from molecular dynamics and In-Vitro studies Frontiers in Oncology colorectal cancer cytotoxic T lymphocyte Dickkopf-like 1 protein F-box protein 39 Opa-interacting protein 5 Toll-Like Receptor 4 |
| title | Design and immunogenic evaluation of multi-epitope vaccines for colorectal cancer: insights from molecular dynamics and In-Vitro studies |
| title_full | Design and immunogenic evaluation of multi-epitope vaccines for colorectal cancer: insights from molecular dynamics and In-Vitro studies |
| title_fullStr | Design and immunogenic evaluation of multi-epitope vaccines for colorectal cancer: insights from molecular dynamics and In-Vitro studies |
| title_full_unstemmed | Design and immunogenic evaluation of multi-epitope vaccines for colorectal cancer: insights from molecular dynamics and In-Vitro studies |
| title_short | Design and immunogenic evaluation of multi-epitope vaccines for colorectal cancer: insights from molecular dynamics and In-Vitro studies |
| title_sort | design and immunogenic evaluation of multi epitope vaccines for colorectal cancer insights from molecular dynamics and in vitro studies |
| topic | colorectal cancer cytotoxic T lymphocyte Dickkopf-like 1 protein F-box protein 39 Opa-interacting protein 5 Toll-Like Receptor 4 |
| url | https://www.frontiersin.org/articles/10.3389/fonc.2025.1592072/full |
| work_keys_str_mv | AT peiweisun designandimmunogenicevaluationofmultiepitopevaccinesforcolorectalcancerinsightsfrommoleculardynamicsandinvitrostudies AT luolinwang designandimmunogenicevaluationofmultiepitopevaccinesforcolorectalcancerinsightsfrommoleculardynamicsandinvitrostudies AT zhongliu designandimmunogenicevaluationofmultiepitopevaccinesforcolorectalcancerinsightsfrommoleculardynamicsandinvitrostudies AT zhengleixu designandimmunogenicevaluationofmultiepitopevaccinesforcolorectalcancerinsightsfrommoleculardynamicsandinvitrostudies |